Saturday, March 31, 2012

Here’s What That New UCSF Paper Says in Plain English (And Why Evolution Needs Another Do-Over)

If you had a four-letter alphabet and all words were three letters, then how many words would there be? The answer is 4 times 4 times 4, or 4-cubed, or 4^3, or 64. That’s how the DNA code works. Our DNA has four molecular “letters” and to create a protein the letters are taken three at a time in words called “codons.” Each codon specifies an amino acid and these 64 different codons are mapped to 20 different amino acids (and a “stop” signal). Since the 64 different codons far exceeds the 20 different amino acids and the stop signal, the code is degenerate. In other words, there are multiple codons that map the same amino acid (just as “absurd” and “ludicrous” have similar meanings).

But why the mismatch? If only 20 different amino acids are coded for, why are there 64 different codons? There is quite a bit of unused messaging power, or what engineers call “bandwidth.” According to evolutionists, it was just another biological kludge revealing nature’s dysteleology.

But ever since its discovery the DNA code has continued to yield hidden treasures of intricacy. For example, the code is cleverly designed at several levels, including minimizing the effects of errors and maximizing information content (such as in supporting overlapping messages).

Furthermore the code’s unused bandwidth has been found to be used in a variety of creative ways where additional information is layered on the basic message indicating the amino acid sequence. You can see some examples here, here, here and here.

The new UCSF paper is another such an example of yet another layer of information in the “unused” bandwidth that evolutionists thought was just an inefficient fluke. It has been known for years that a DNA gene, that is used to construct a protein, has some special signals near the beginning that will help the translating process get started correctly.

Now, the new research indicates that similar signals are used throughout the gene. Their purpose is not to help the protein production process get started correctly, but rather to fine-tune the speed of the production process.

It is yet another example of the many different types of information that are layered in a DNA gene which have evolutionists rewriting their script and explaining that “It’s over. None of that happened.”

“Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible”Donald E. Johnson – Bioinformatics: The Information in Life

Yet despite this severe constraint on evolability, it is found that DNA is a 'optimal code';

Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature. (Fazale Rana, -The Cell's Design - 2008 - page 177)

“The genetic code’s error-minimization properties are far more dramatic than these (one in a million) results indicate. When the researchers calculated the error-minimization capacity of the one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution. Researchers estimate the existence of 10^18 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This means of 10^18 codes few, if any have an error-minimization capacity that approaches the code found universally throughout nature.” Fazale Rana - From page 175; 'The Cell’s Design' http://www.reasons.org/biology/biochemical-design/fyi-id-dna-deciphering-design-genetic-code

As well there was a ‘optimality’ found for the 20 amino acid set used in the 'standard' Genetic code when the set was compared to 1 million randomly generated alternative amino acid sets;

Does Life Use a Non-Random Set of Amino Acids? - Jonathan M. - April 2011 Excerpt: The authors compared the coverage of the standard alphabet of 20 amino acids for size, charge, and hydrophobicity with equivalent values calculated for a sample of 1 million alternative sets (each also comprising 20 members) drawn randomly from the pool of 50 plausible prebiotic candidates. The results? The authors noted that: "…the standard alphabet exhibits better coverage (i.e., greater breadth and greater evenness) than any random set for each of size, charge, and hydrophobicity, and for all combinations thereof." http://www.evolutionnews.org/2011/04/does_life_use_a_non-random_set045661.html

Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement – 2009 Excerpt: A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. http://pre.aps.org/abstract/PRE/v79/i6/e060901

Collective evolution and the genetic code - 2006:Excerpt: The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving.http://www.pnas.org/content/103/28/10696.full

Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes.... the present findings support the view that protein-coding regions can carry abundant parallel codes.http://genome.cshlp.org/content/17/4/405.full

The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (12 different ways of DNA transcription) (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford - Genetic Entropy

DNA coding is apparently successfully designed along the very stringent guidelines laid out by Landauer's principle of 'reversible computation' in order to achieve such amazing energy efficiency, something man has yet to accomplish in any meaningful way for computers:

Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. BennettExcerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus (computers), dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,,http://www.hep.princeton.edu/~mcdonald/examples/QM/bennett_shpmp_34_501_03.pdf

Life Leads the Way to Invention - Feb. 2010Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “ In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale.http://creationsafaris.com/crev201002.htm#20100226a

As well DNA is optimized for protection from UV radiation;

DNA Optimized for PhotostabilityExcerpt: These nucleobases maximally absorb UV-radiation at the same wavelengths that are most effectively shielded by ozone. Moreover, the chemical structures of the nucleobases of DNA allow the UV-radiation to be efficiently radiated away after it has been absorbed, restricting the opportunity for damage.http://www.reasons.org/dna-soaks-suns-rays

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome - Oct. 2009Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.http://www.sciencemag.org/cgi/content/abstract/326/5950/289

3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.http://www.sciencedaily.com/releases/2009/10/091008142957.htm

Do you believe Richard Dawkins exists?Excerpt: DNA is the best information storage mechanism known to man. A single pinhead of DNA contains as much information as could be stored on 2 million two-terabyte hard drives.http://creation.com/does-dawkins-exist

This is all still essentially argument by analogy. The fact that what happens in the genome can be modeled in terms of a code does mean it is one with all the implications of an intelligent cryptographer. As the philosopher John S Wilkins wrote in his paper A deflation of genetic information

Nobody can sensibly argue that because Maynard Smith was able to apply game theory mathematics to evolutionary genetics (Maynard Smith 1979, 1982) that we must suppose that genes actually play games, or have interests, or compute their payoff-loss matrices...

A code implies both a coder and a decoder. Darwinists reluctantly accept code and decoder but deny the need for a coder. They believe that the code coded itself! This is no better than some Christians believing that wine can literally turn into the blood of Jesus. How Darwinists get away with such in-your-face nonsense boggles the mind.

That's precisely it, pinhead. There is no difference between a computer program code and a genetic code. They are both abstract codes with meaning that is designed to be deciphered by a separate mechanism or an intelligent agent. A code implies intent and intent implies intelligence.

Answer me this, bonobo face. Which came first, the code or the decoder? LOL. Get a clue.

Skeptic's Objection to Information Theory #1: - "DNA is Not a Code"Summary:1. Code is defined as the rules of communication between an encoder (a “writer” or “speaker”) and a decoder (a “reader” or “listener”) using agreed upon symbols.2. DNA’s definition as a literal code (and not a figurative one) is nearly universal in the entire body of biological literature since the 1960′s.3. DNA code has much in common with human language and computer languages4. DNA transcription is an encoding / decoding mechanism isomorphic with Claude Shannon’s 1948 model: The sequence of base pairs is encoded into messenger RNA which is decoded into proteins.5. Information theory terms and ideas applied to DNA are not metaphorical, but in fact quite literal in every way. In other words, the information theory argument for design is not based on analogy at all. It is direct application of mathematics to DNA, which by definition is a code.http://cosmicfingerprints.com/dnanotcode.htm

http://www.cosmicfingerprints.com/wp-content/uploads/2011/01/shannon_comm_channel.jpgClaude Shannon’s communication model (From The Mathematical Theory of Communication, University of Illinois Press, 1998).http://www.cosmicfingerprints.com/wp-content/uploads/2011/01/dna_isomorphic.jpgHubert Yockey’s DNA communication channel model. Notice that it contains the exact same components as Shannon’s – the two systems are isomorphic.

T: Code also means any process where the inputs map to the outputs. DNA is a code in that sense,but DNA is not an abstract code.

Care to tell us why CTAG is not an abstract code?

Sure. An abstract code makes use of arbitrarily defined symbols to pass information. An example is Morse code, where arbitrary grouping of dots and dashes are used to represent letters.

The molecules CTAG are not arbitrary symbols. Their chemistry is an integral part of a very complicated chemical reaction, the end result of which is a protein. You can't make a strand of DNA from modeling clay and have it form a clay protein.

It's the abstract, arbitrary part that always confuses Creationists. You need an intelligent encoder/decoder to use abstract, arbitrary symbols. You don't need them for a chemical reaction like DNA.

It's the abstract, arbitrary part that always confuses Creationists. You need an intelligent encoder/decoder to use abstract, arbitrary symbols. You don't need them for a chemical reaction like DNA.

What a maroon. Jumping up and down and foaming at the mouth while insisting that DNA is not an abstract and arbitrary code is not a valid argument unless you are a moron.

DNA code is arbitrary and abstract because the gene that codes for echolocation in bats, for example, could have been coded differently. What makes it an arbitrary code is that both coder and decoder agree on the meaning of the code.

DNA code is arbitrary and abstract because the gene that codes for echolocation in bats, for example, could have been coded differently.

Then demonstrate it, don't just assert it.

What makes it an arbitrary code is that both coder and decoder agree on the meaning of the code.

LOL! OK fruit loop, do this experiment. Recreate a bat's echolocation genes out of Lego or Tinker Toys. Then get them to react on their own and create Lego or Tinker Toy proteins. If it's arbitrary as you say then you should have no problem. Let us know the results.

Fair enough. So what are the physical representations of the symbols in morse code which make morse code intelligible?

If the code is being sent audibly it's a long tone (0.6 sec) for a dash, a shorter tone (0.2 sec) for a dot. In print form it's the character dash ( - ) or a dot ( . ) It can also be sent visually (between ships using lanterns for example) with a longer flash for the dash, shorter flash for the dot.

Listen here, bonobo face, and listen carefully. I know you only have two neurons between your ears but give it a try anyway.

There are 20 different codes for twenty different amino acids. The codes are arbitrary because each code could represent a different amino acid than it currently does. What matters is how the code interpreter is programmed to interpret each code.

Your Lego and Tinker Toy experiment does not surprise me. It's just the sort of nonsense I would expect from a moron like you. Do you even understand the concept of a programming language and a language interpreter or compiler? I doubt it. You're just busy kissing rear ends as you usually do.

Then demonstrate it fruit loop. Don't just flap your fruit loop gums. Demonstrate that any arbitrary arrangement of codons can produce any amino acid.

There is nothing to demonstrate, bonobo face. It is common knowledge that there are variants to the standard genetic code. IOW, a code can mean a different thing in certain cases. For example, human mitochondrial genes use a variation of the standard code (Wikipedia article). Even the stop codon can be different in different organisms.

This variability in the meaning of certain codes is proof of the arbitrary and abstract nature of the genetic code. It is proof that the code designers decided on the specific meaning of the genetic code in an arbitrary fashion.

So what? That does not make a chemical reaction a code. The code has to do with the meaning of the codons, moron. Variability means that a codon can mean one thing for one interpreter and another for a different interpreter. It's abstract and arbitrary, moron.

Game over fruit loop. Thanks for playing.

Only in your dreams, bonobo face, only in your dreams. The game is just starting. There are plenty of asteroid orifices for you to kiss. LOL. Bonobo face needs to get a clue.

As usual, what you "understand" is dead wrong. The genetic code used by all know life forms is virtually identical with a few slight variations in things like stop codons. That is out of 1.5x10^84 *possible* mappings of amino acids to triplet codons.

Translation between codons and amino acids they produce is 100% determined by chemistry, and the relationship between codons and the amino acids certainly isn't arbitrary.

Bonobo face never misses an opportunity to put both feet in his/her mouth. The truth is that codons don't just code for proteins. They also code for all sort control functions that govern the timing of the expressions of various genes.

Every time you see an evolutionist repeat something over and over (like the way they use to repeat the lie of nested hierarchies as proof of evolution over and over), you can be 99% certain it's a lie. This "100% chemistry" is a good example of another repeated lie. It's like saying that, since a program in computer memory consists of low and high voltages, and since it's all governed by electromagnetism, therefore it is not a code.

The silliness and dishonesty of evolutionists is blatant and in your face. The crap that pours out their lying mouths would fill the Mariana trench.

By the way, what happened to that Zachriel idiot? He was one of the fiercest promoters of the nested hierarchy lie. Has he finally been silenced or did he commit suicide out of shame? LOL.

We're still waiting for your proof that since a program is 100% electromagnetic, therefore it is not a code. Your stupidity must be coded in your DNA. You must have inherited too many bonobo genes that code for stupidity. LOL.

Don't lie. You certainly claim that DNA is not an abstract code because translation between codons and amino acids they produce is 100% determined by chemistry. Therefore, to imitate your stupid and flawed logic, by analogy, a computer program is not code either, since its working is 100% determined by electromagnetism. How stupid can you get, bonobo face? But then again, that analogy might be too hard for you to grasp, what with the 2 neurons between your bonobo ears? LOL.

Go ahead and demonstrate it by producing aspartic acid from the CAG triplet. Or by producing glycine from the AAC triplet.

I need to do no such thing although I don't see why it cannot be done. All I need to show is that DNA can code for all sorts of things and that those things are not necessarily amino acids. In fact, the same code can represent different things even within the same genome.

According to you the mapping has nothing to do with chemistry, remember?

I never said that. You lie as you always do. Why? Because you are an evolutionist. Lying is what you do. Everything you say is a lie. I also never said that a program has nothing to do with electromagnetism. Oops. Here's that incomprehensible analogy again.

To your eternal sorrow, bonobo face, you and your band of pathetic liars don't put food on my table. I am proud to be the target of your ridicule. I would not have it any other way. You can all kiss my you know what.

Have you thought this through? Maybe you shouldn't so glibly mock your fellow Christians.

1. I don't worship the Bible. That would be idolatry. The Bible is just one of many research tools that I use.

2. If Jesus did say those words, it is obvious he was speaking allegorically.

3. Paul was a human being. Whether or not he was chosen by the master to preach to the gentiles, he was still a fallible human being. I don't have to believe everything he said or wrote. Heck, some of the letters attributed to Paul may not have been written by him.

4. I kiss nobody's behind except my master's. And by nobody, I especially mean Christians and organized Christian religions. Even though I am a Christian, I blame them for keeping more people away from Christianity than any other group, including atheists. However, the atheists have no excuse because they portray themselves as the champions of reason. They are not.

Information Theory, Evolution, and the Origin of Life - Hubert P. Yockey, 2005 Excerpt: “Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.” http://www.cambridge.org/catalogue/catalogue.asp?isbn=9780521802932&ss=exc

Information Theory, Evolution, and the Origin of Life - Hubert P. Yockey, 2005 “The belief of mechanist-reductionists that the chemical processes in living matter do not differ in principle from those in dead matter is incorrect. There is no trace of messages determining the results of chemical reactions in inanimate matter. If genetical processes were just complicated biochemistry, the laws of mass action and thermodynamics would govern the placement of amino acids in the protein sequences.” Let me provide the unstated conclusion: But they don’t. http://www.uncommondescent.com/intelligent-design/living-things-machines-and-intelligent-design-part-two-of-a-response-to-the-smithy/#comment-353336

A New Design Argument - Charles ThaxtonExcerpt: "There is an identity of structure between DNA (and protein) and written linguistic messages. Since we know by experience that intelligence produces written messages, and no other cause is known, the implication, according to the abductive method, is that intelligent cause produced DNA and protein. The significance of this result lies in the security of it, for it is much stronger than if the structures were merely similar. We are not dealing with anything like a superficial resemblance between DNA and a written text. We are not saying DNA is like a message. Rather, DNA is a message. True design thus returns to biology."http://www.arn.org/docs/thaxton/ct_newdesign3198.htm

Judge Rules DNA is Unique (and not patentable) Because it Carries Functional Information - March 2010“Today the idea that DNA carries genetic information in its long chain of nucleotides is so fundamental to biological thought that it is sometimes difficult to realize the enormous intellectual gap that it filled.... DNA is relatively inert chemically.”http://www.uncommondescent.com/intelligent-design/judge-rules-dna-is-unique-because-it-carries-information/

Upright Biped Replies to Dr. Moran on “Information” - December 2011 Excerpt: 'a fair reading suggests that the information transfer in the genome shouldn’t be expected to adhere to the qualities of other forms of information transfer. But as it turns out, it faithfully follows the same physical dynamics as any other form of recorded information.' http://www.uncommondescent.com/intelligent-design/upright-biped-replies-to-dr-moran-on-information/

Even the leading "New Atheist" in the world, Richard Dawkins, agrees that DNA functions exactly like digitally coded information:

Information Theory, Evolution, and the Origin of Life - Hubert P. Yockey, 2005 Excerpt: “Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.”

We can all assemble a collection of cut-and-paste quotes. I parry with this from the John Wilkins paper:

In line with several cautionary assessments of genetic information in biology (Griesemer 2005; Jablonka 2002; Griffiths 2001; Godfrey Smith 2000b; Maclaurin 1998; Oyama 1985), I want to consider whether information talk is entirely appropriate. Unlike these commentators, however, I wish to make the following further claims – that the use of genetic information in biological contexts often boils down essentially to a causal correlation between physical aspects of genetic processes, including direct causation, and that the remainder, including teleosemantic accounts of genetic information, are representation-driven, and are thus best conceived of as “information in the head”. This means we can dispense with genetic information in our ontology of the biological world, and rest content with it as a property of our representations of that world. The primary issue here is what the ontological standing of genetic information is within biology. We can grant that it has an inevitable heuristic role in science, as Sarkar (2000) notes, but the pressing question is whether it has, as he puts it, a substantive or ontological role.

And since you're playing Yockey again

Information Theory, Evolution, and the Origin of Life - Hubert P. Yockey, 2005 “The belief of mechanist-reductionists that the chemical processes in living matter do not differ in principle from those in dead matter is incorrect. There is no trace of messages determining the results of chemical reactions in inanimate matter. If genetical processes were just complicated biochemistry, the laws of mass action and thermodynamics would govern the placement of amino acids in the protein sequences.” Let me provide the unstated conclusion: But they don’t.

I will counter with another Wilkins gambit:

ABSTRACT: It is often claimed there is information in some biological entity or process, most especially in genes. Genetic “information” refers to distinct notions, either of concrete properties of molecular bonds and catalysis, in which case it is little more than a periphrasis for correlation and causal relations between physical biological objects (molecules), or of abstract properties, in which case it is mind-dependent. When information plays a causal role, nothing is added to the account by calling it “information”. In short, if genetic information is concrete, it is causality. If it is abstract, it is in the head.

Falsification Of Neo-Darwinism by Quantum Entanglement/Informationhttps://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US

,,,Encoded ‘classical’ information such as what Dembski and Marks demonstrated the conservation of, and such as what we find encoded in computer programs, and yes, as we find encoded in DNA, is found to be a subset of ‘transcendent’ (beyond space and time) quantum entanglement/information by the following method:,,,

,,,This following research provides solid falsification for the late Rolf Landauer’s decades old contention that the information encoded in a computer is merely physical (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it;

Quantum knowledge cools computers: New understanding of entropy – June 2011Excerpt: No heat, even a cooling effect;In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.”http://www.sciencedaily.com/releases/2011/06/110601134300.htm

,,,And to dot the i’s, and cross the t’s, here is the empirical confirmation that quantum information is in fact ‘conserved’;,,,

Quantum no-hiding theorem experimentally confirmed for first timeExcerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html

Falsification Of Neo-Darwinism by Quantum Entanglement/Informationhttps://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US

Yes, I know. There are weird and wonderful things happening at the quantum level but none of them necessarily provide comfort and support for either of us. Reading some of the discussions about these phenomena, it's apparent that even the experts in the field are struggling to make sense of what they are seeing. Neither of us are quantum physicists so any conclusions either of us draw from the little we understand could be way wide of the mark.

For example, on the question of information, Dembski himself quoted a list of some forty separate definitions compiled by Jack Szostak. Which one of those are you talking about?

As for quantum entanglement, I noticed in the discussions about Leggett inequalities that it may be misleading to think of entangled particle pairs as two discrete entities passing "information" themselves instantaneously, that perhaps it might be better to conceive of them as a single extended entity.

And fascinating as quantum phenonomena undoubtedly are, they do not appear to translate directly up into our macroscopic world. If a billiards player puts two white balls on the table and sends one spinning across the table into a corner pocket, we do not see the other ball simultaneously go into a reverse spin across the table and down the opposite corner pocket. I assume that you or any of the other people I know do not cease to exist the moment I stop being conscious of you and I'm pretty sure I continue to be in spite of the fact that Alain Aspect is almost certainly unaware that I exist at all.

Quantum phenomena are undoubtedly weird in the extreme, but if the experts are still trying to make sense of them then its presumptuous of you- to say the least - to infer that they provide any support for your religious beliefs.

Ian, regardless of what you don't understand of Quantum Mechanics, the fact is that Quantum Mechanics has established information as its own independent entity. A independent entity that is beyond space and time and which exercises dominion of matter-energy. Moreover, Quantum Mechanics has unambiguously falsified reductive materialism, which is the foundation Darwinism is built on, as the true description of reality.

notes:

Quantum Evidence for a Theistic Universehttps://docs.google.com/document/d/1agaJIWjPWHs5vtMx5SkpaMPbantoP471k0lNBUXg0Xo/edit

Three intersecting lines of experimental evidence from quantum mechanics that shows that consciousness precedes material realityhttps://docs.google.com/document/d/1G_Fi50ljF5w_XyJHfmSIZsOcPFhgoAZ3PRc_ktY8cFo/edit

'Dembski himself quoted a list of some forty separate definitions compiled by Jack Szostak. Which one of those are you talking about?'

Well why don't we use the one that Jack Szostak himself developed to deal with functional sequence complexity in biology?

It has now been demonstrated that the specific sequence complexity, of a functional protein, can be mathematically quantified as functional information bits(Fits).

Functional information and the emergence of bio-complexity: Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak: Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define 'functional information,' I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions. http://genetics.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Hazen_etal_PNAS_2007.pdf

Measuring the functional sequence complexity of proteins - Kirk K Durston, David KY Chiu, David L Abel and Jack T Trevors - 2007 Excerpt: We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families.,,, http://www.tbiomed.com/content/4/1/47

Intelligent Design: Required by Biological Life? K.D. Kalinsky - Pg. 10 - 11Case Three: an average 300 amino acid protein:Excerpt: It is reasonable, therefore, to estimate the functional information required for the average 300 amino acid protein to be around 700 bits of information. I(Ex) > Inat and ID (Intelligent Design) is 10^155 times more probable than mindless natural processes to produce the average protein.http://www.newscholars.com/papers/ID%20Web%20Article.pdf

Book Review - Meyer, Stephen C. Signature in the Cell. New York: HarperCollins, 2009.Excerpt: As early as the 1960s, those who approached the problem of the origin of life from the standpoint of information theory and combinatorics observed that something was terribly amiss. Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created. Now of course, elementary particles aren't chemical laboratories, nor does peptide synthesis take place where most of the baryonic mass of the universe resides: in stars or interstellar and intergalactic clouds. If you look at the chemistry, it gets even worse—almost indescribably so: the precursor molecules of many of these macromolecular structures cannot form under the same prebiotic conditions—they must be catalysed by enzymes created only by preexisting living cells, and the reactions required to assemble them into the molecules of biology will only go when mediated by other enzymes, assembled in the cell by precisely specified information in the genome.So, it comes down to this: Where did that information come from? The simplest known free living organism (although you may quibble about this, given that it's a parasite) has a genome of 582,970 base pairs, or about one megabit (assuming two bits of information for each nucleotide, of which there are four possibilities). Now, if you go back to the universe of elementary particle Planck time chemical labs and work the numbers, you find that in the finite time our universe has existed, you could have produced about 500 bits of structured, functional information by random search. Yet here we have a minimal information string which is (if you understand combinatorics) so indescribably improbable to have originated by chance that adjectives fail.http://www.fourmilab.ch/documents/reading_list/indices/book_726.html

'And fascinating as quantum phenomena undoubtedly are, they do not appear to translate directly up into our macroscopic world.'

Yet,,,

LIVING IN A QUANTUM WORLD - Vlatko Vedral - 2011Excerpt: Thus, the fact that quantum mechanics applies on all scales forces us to confront the theory’s deepest mysteries. We cannot simply write them off as mere details that matter only on the very smallest scales. For instance, space and time are two of the most fundamental classical concepts, but according to quantum mechanics they are secondary. The entanglements are primary. They interconnect quantum systems without reference to space and time. If there were a dividing line between the quantum and the classical worlds, we could use the space and time of the classical world to provide a framework for describing quantum processes. But without such a dividing line—and, indeed, with­out a truly classical world—we lose this framework. We must ex­plain space and time (4D space-time) as somehow emerging from fundamental­ly spaceless and timeless physics.http://phy.ntnu.edu.tw/~chchang/Notes10b/0611038.pdf

Now Ian if you want to refute the experimental proof I just cited you must experimentally falsify quantum non-locality first, and then experimentally falsify Abel's null hypothesis second! Cutting and pasting opinions will not cut it!

The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”http://www-qa.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html

"The color of many fruits and vegetables codes to the freshness. Bananas are green when unripe, yellow when ripe, brown or black when overripe.

Did the Intelligent Banana Designer create that color coded mapping?"

That code it is also abstract, I can draw a green banana with a piece of chalk, near a yellow banana and black banana and my six year old son can say which of that he would eat. Also I can make plastic colored bananas and the monkeys will choose the right ones. You do not need the real banana to send the message to receiver. So it is abstract.

"No. There is no abstraction at all anywhere in the DNA-->protein process. None."

Yes, there is, read Biochemistry by Lehninger. You can substitute the codon in tRNA and the ribosome will put the wrong aminoacid. There is no chemical relation between the aa and the codon. So tRNA is an arbitrary link between the order of three bases on it and 20 aminoacids.

Perhaps you are missing the point, the reason the banana is green or brown is not to communicate its freshness. It is chemistry, it is not an abstract code.Unless you believe either that banana itself is capable of coding itself or the most powerful being imaginable cares whether monkeys eat unripe bananas, you have no coder.

T: "The color of many fruits and vegetables codes to the freshness. Bananas are green when unripe, yellow when ripe, brown or black when overripe.

That code it is also abstract, I can draw a green banana with a piece of chalk, near a yellow banana and black banana and my six year old son can say which of that he would eat. Also I can make plastic colored bananas and the monkeys will choose the right ones. You do not need the real banana to send the message to receiver. So it is abstract

No Blas. If you draw colored bananas with chalk then you have created a new abstract code using your drawings as arbitrarily defined symbols. That doesn't make the original fruit colors be abstract.

It's the same with DNA. Humans use the arbitrarily chosen symbols CTAG as abstract representation of certain chemical molecules, but that doesn't make the chemical molecules themselves be abstract, arbitrary symbols.

You are mistaking the map for the territory, an all too common Creationist blunder.

Isn;t the fruit signaling that it is ripe because it "wants" to be eaten? When an animal eats a fruit, it scatters the seeds. So, the fruit is using color coding to communicate to animals. So it is an abstract code.

Isn;t the fruit signaling that it is ripe because it "wants" to be eaten? When an animal eats a fruit, it scatters the seeds. So, the fruit is using color coding to communicate to animals. So it is an abstract code.

"It's the same with DNA. Humans use the arbitrarily chosen symbols CTAG as abstract representation of certain chemical molecules, but that doesn't make the chemical molecules themselves be abstract, arbitrary symbols."

Can you explain the non arbitrary link between AGG ans Arginine, GGA and Glycine and UGA ans none of the 20 aminoacids?

Are you really don´t seeing the difference? Are you really foolling yourself in that way? There is no other option for sodium an chloride to form sodium chloride. When you have arnininil-tRNA there are 64 options in which order in the protein it can be inserted. The difference is the spatial order of the three bases G,G and A. Which chemical or physical law establish a difference between AGG and GGA?

The difference is the spatial order of the three bases G,G and A. Which chemical or physical law establish a difference between AGG and GGA?

The physical properties of the molecules themselves cause different types of molecular bonding to occur. The alternating phosphate and sugar molecules of the DNA backbone are held together by phosphodiester bonding. Phosphodiester bonds are not symmetrical and thus give the DNA strand a direction. The double spiral is kept stable by hydrogen bonds and noncovalent interactions known as pi stacking.

The physical structure of the three base codon and the order of its nucleotides make a big difference in how it is translated. That's why AGG and GGA don't produce the same amino acid.

The difference is the spatial order of the three bases G,G and A. Which chemical or physical law establish a difference between AGG and GGA?

Bonobo face responded:

The physical structure of the three base codon and the order of its nucleotides make a big difference in how it is translated. That's why AGG and GGA don't produce the same amino acid.

Amazing. Of course it makes a difference and of course it has to do with chemistry and that's exactly what Blas said. But so what if it's a chemical process that is used to decode the DNA strand? Obviously, the decoder is programmed to decipher the order and composition of the strand and respond accordingly. And again, there are huge numbers of strands that do not code for amino acids but represent specialized control functions that are needed during development and adaptation.

The cretinous crap that bonobo face is pushing here is analogous to the following:

Since a computer program in computer memory consists of EM potentials and since the computer uses 100% EM principles to run the program, therefore the program is not based on an abstract code.

This is silly to the extreme. What I want to know is why bonobo face is so darn stupid?

Obviously, the decoder is programmed to decipher the order and composition of the strand and respond accordingly.

More empty assertions, no demonstration from the fruit loop.

Since a computer program in computer memory consists of EM potentials and since the computer uses 100% EM principles to run the program, therefore the program is not based on an abstract code.

Wrong again fruit loop. The same human written computer code can be run on any number of devices with different physical and electrical characteristics. It can even be executed on a large abacus. It is not part of and dependent on the physical substrate. DNA is.

Wrong again fruit loop. The same human written computer code can be run on any number of devices with different physical and electrical characteristics. It can even be executed on a large abacus. It is not part of and dependent on the physical substrate. DNA is.

LOL. What a moron. It is entirely possible, in principle, to take the genome of any organism and simulate it on a digital computer that is powerful enough. All physical systems are Turing compatible.

It is entirely possible, in principle, to take the genome of any organism and simulate it on a digital computer that is powerful enough.

Your problem isn't to simulate the process fruit loop. Your problem is to actually make a Lego DNA strand be able to produce a functioning Lego protein. You can't of course, because DNA isn't an abstract code. But you're way too loopy to understand

How stupid can you get? If a code can be stored on paper or magnetic memory or used to create a program in a computer, it is an abstract code. Your problem, bonobo face, is that your stupid allegiance to your stupid religion makes you stupid as sh!t. LOL

How stupid can you get? If a code can be stored on paper or magnetic memory or used to create a program in a computer, it is an abstract code.

Psst..hey angry dummy...once again you're too stupid to understand the difference between the human designed abstract language to describe the DNA chemical reaction which can be stored, and the non-abstract DNA molecules themselves that can't.

"Go ahead and demonstrate it by producing aspartic acid from the CAG triplet. Or by producing glycine from the AAC triplet."

Already done Thorton, take the glycinil-tRNA and change the glycine triplet for AAC, use this as unique surce of glycine and you will get Glicyne for any AAC in the DNA.

"The physical properties of the molecules themselves cause different types of molecular bonding to occur. The alternating phosphate and sugar molecules of the DNA backbone are held together by phosphodiester bonding. Phosphodiester bonds are not symmetrical and thus give the DNA strand a direction. The double spiral is kept stable by hydrogen bonds and noncovalent interactions known as pi stacking."

You know that the triplet do not interact with aminozcid binding site of the tRNA. But you keep saying this stupid thing that the genetic code is not arbitrary. You know that the chemistry of the 20 aminoacids and the 4 bases do not allow a 100% unique relation between any combination of them, but you keep saying that the genetic code it is not arbitrary. And I have to believe to darwinist that evolution is a fact?

You know that the chemistry of the 20 aminoacids and the 4 bases do not allow a 100% unique relation between any combination of them, but you keep saying that the genetic code it is not arbitrary.

Like I pointed out to the fruit loop above: just because different chemical reactions can produce the same result doesn't make the reactants arbitrary. If the mapping was truly arbitrary then you could create ANY amino acid out of ANY triplet. But you can't.

Amazing that you IDCers can't wrap your mind around such a simple concept.

"Like I pointed out to the fruit loop above: just because different chemical reactions can produce the same result doesn't make the reactants arbitrary. If the mapping was truly arbitrary then you could create ANY amino acid out of ANY triplet. But you can't."

The genetic do not create aminoacids, the genetic code are the instructions to put the right aminoacid in th reight place. I alredy told you that you can change the codon and it still works, it is old news biochemistry text books of the seventies. Please take the pill and then try to read again.

Has it been demonstrated that the laws of chemistry will not allow different combinations of triplets to code for different amino acids. Is the any reason why the laws of chemistry won't allow, for example, AGG and CGG to code for other amino acids than the ones they do. If they can't, then why not? The difference is that they bond to specific tRNA's. Why can't they bond to different tRNA's in a different coding system. Its like the laws of electronics and computer science allow the same computer to use both ASCII and EPSIDIC. The exact coding system chosen is arbitrary.

I didn't say any reactant can produce any product. I just don't know of any reason why the same laws that allow for one code can't allow for another. The same laws should allow AGG to code for the same amino acid as GGA. The same laws of electronics and computer science allow you to write code in Fortran and Cobol. (Am I dating myself with my CS references?. It's been a long time.)

I don't know what you mean by "forces" in the above post. I do know that the laws of physics allow for different computer codes. The laws of pencil and paper, cunieform and papyrus allow for different alphabets, which are codes. I'm asking why the laws of chemistry can't allow for different genetic codes.